Psyllid ID: psy7154

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-----

MKYVVLYPDKEETKWKIINWNDNLVPVEKQIRNMVINFGPQHPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNVIGMKEMRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSEMKGYPVPPGATYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAIIDPHIGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVMFTFYQWAAQVLT

cccccccccccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHccEEEccHHHHHHHcccccccccccccccccccccccccccccccccccccccEEEHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccEEcccccccccEEEEEEccccccEEEEEccccccHHHHHHHHHcccccccHHHHHcccccccccHHHHHHHccccccccccccccHHHHHcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccc

ccEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccHHHHHHcccccccccccccHHHHHHHHHHHcHHHHHHHHHHHccccEEEEEEcccEEEcHHHHHHccccccEEEcccccHcHccccccHHHccccEcccccccccEEEHHHHHHHHHHHHHHHHHcccccEEEcccccccccHHHccccEcccccEEEEEEcccccEEEEEEEccccccEEEEEccccHHHHHHHHHHHccccccEEEEEEcHHHcHHccHHHHHHHHHHHHHHccHHcHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcc

mkyvvlypdkeetkwkiinwndnlvPVEKQIRNMVinfgpqhpaaHGVLLLFAEITRILNHIMAVGthaldvgamtpfFWLFEEREKMMEFYERASGARMHaayvrpggvaldipigllDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDalnygfsgvmlrgsgikwdlrkvqpydgyenfefdipigthgnvIGMKEMRQSLRIVEQAINkmpggevrtddmkistpsrsemkgypvppgatytaveapkgefgVYLVsdgtskpyrckikapgfAHLAALEKIGKGSFLADIVAIIdphigllhrGTEKLIEYKTYtqalpyfdrldyvSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVMFTFYQWAAQVLT

mkyvvlypdkeetkwkiinwndNLVPVEKQIRNMVINFGPQHPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNVIGMKEMRQSLRIVEQAinkmpggevrtddmkistpsrsemkgypvPPGATYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAIIDPHIGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVMFTFYQWAAQVLT

**YVVLYPDKEETKWKIINWNDNLVPVEKQIRNMVINFGPQHPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNVIGMKEMRQSLRIVE***********************************TYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAIIDPHIGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVMFTFYQWAAQV**

****VLYPDKEETKWKIINWNDNLVPVEKQIRNMVINFGPQHPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNVIGMKEMRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSEMKGYPVPPGATYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAIIDPHIGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIEVPLRAKYIRVMFTFYQWAAQVLT

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		385	2.2.26 [Sep-21-2011]
Q641Y2		463	NADH dehydrogenase [ubiqu	yes	N/A	0.711	0.591	0.674	1e-115
Q91WD5		463	NADH dehydrogenase [ubiqu	yes	N/A	0.711	0.591	0.674	1e-115
P17694		463	NADH dehydrogenase [ubiqu	yes	N/A	0.711	0.591	0.664	1e-113
Q0MQG3		463	NADH dehydrogenase [ubiqu	N/A	N/A	0.711	0.591	0.657	1e-108
Q0MQG4		463	NADH dehydrogenase [ubiqu	N/A	N/A	0.711	0.591	0.657	1e-108
Q0MQG5		463	NADH dehydrogenase [ubiqu	yes	N/A	0.711	0.591	0.657	1e-108
O75306		463	NADH dehydrogenase [ubiqu	yes	N/A	0.711	0.591	0.657	1e-108
O21270		396	NADH-ubiquinone oxidoredu	N/A	N/A	0.688	0.669	0.638	1e-104
Q37619		400	NADH-ubiquinone oxidoredu	N/A	N/A	0.688	0.662	0.614	1e-101
Q93873		482	Probable NADH dehydrogena	no	N/A	0.672	0.537	0.630	1e-101

>sp\|Q641Y2\|NDUS2_RAT NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Rattus norvegicus GN=Ndufs2 PE=1 SV=1	Back alignment and function desciption

 Score =  416 bits (1068), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 199/295 (67%), Positives = 234/295 (79%), Gaps = 21/295 (7%)

Query: 35  VINFGPQHPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYER 94
           ++N  P  P A  + +LF EITRILNHIMAV THALD+GAMTPFFW+FEEREKM EFYER
Sbjct: 158 LLNIQPP-PRAQWIRVLFGEITRILNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYER 216

Query: 95  ASGARMHAAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVG 154
            SGARMHAAY+RPGGV  D+P+GL+DDIY F   FS R+DEVE+MLT NR+W  RT D+G
Sbjct: 217 VSGARMHAAYIRPGGVHQDLPLGLMDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIG 276

Query: 155 IVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGN-----VIGMKE 209
           +VSAEDALNYGFSGVMLRGSGI+WDLRK QPYD Y+  EFD+PIG+ G+     +  ++E
Sbjct: 277 VVSAEDALNYGFSGVMLRGSGIQWDLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEE 336

Query: 210 MRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSEMK---------------GYPVPPGAT 254
           MRQSLRI+EQ +NKMP GE++ DD K+S P R+EMK               GY VPPGAT
Sbjct: 337 MRQSLRIIEQCLNKMPPGEIKVDDAKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGAT 396

Query: 255 YTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII 309
           YTA+EAPKGEFGVYLVSDG+S+PYRCKIKAPGFAHLA L+K+ KG  LAD+VAII
Sbjct: 397 YTAIEAPKGEFGVYLVSDGSSRPYRCKIKAPGFAHLAGLDKMSKGHMLADVVAII 451

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.
Rattus norvegicus (taxid: 10116)
EC: 1EC: .EC: 6EC: .EC: 9EC: 9EC: .EC: 3

>sp\|Q91WD5\|NDUS2_MOUSE NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Mus musculus GN=Ndufs2 PE=1 SV=1	Back alignment and function description

>sp\|P17694\|NDUS2_BOVIN NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Bos taurus GN=NDUFS2 PE=1 SV=2	Back alignment and function description

>sp\|Q0MQG3\|NDUS2_PONPY NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Pongo pygmaeus GN=NDUFS2 PE=2 SV=1	Back alignment and function description

>sp\|Q0MQG4\|NDUS2_GORGO NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Gorilla gorilla gorilla GN=NDUFS2 PE=2 SV=1	Back alignment and function description

>sp\|Q0MQG5\|NDUS2_PANTR NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Pan troglodytes GN=NDUFS2 PE=2 SV=1	Back alignment and function description

>sp\|O75306\|NDUS2_HUMAN NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Homo sapiens GN=NDUFS2 PE=1 SV=2	Back alignment and function description

>sp\|O21270\|NDUS2_RECAM NADH-ubiquinone oxidoreductase 49 kDa subunit OS=Reclinomonas americana GN=NAD7 PE=3 SV=1	Back alignment and function description

>sp\|Q37619\|NDUS2_PROWI NADH-ubiquinone oxidoreductase 49 kDa subunit OS=Prototheca wickerhamii GN=NAD7 PE=3 SV=1	Back alignment and function description

>sp\|Q93873\|NDUS2_CAEEL Probable NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial OS=Caenorhabditis elegans GN=gas-1 PE=3 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		385
357628760		466	NADH dehydrogenase-ubiquinone Fe-S prote	0.672	0.555	0.759	1e-121
195402219		468	GJ13840 [Drosophila virilis] gi\|19415591	0.672	0.553	0.731	1e-120
114051447		466	NADH dehydrogenase-ubiquinone Fe-S prote	0.672	0.555	0.741	1e-119
170051629		469	NADH dehydrogenase iron-sulfur protein 2	0.688	0.565	0.726	1e-119
332373630		461	unknown [Dendroctonus ponderosae]	0.680	0.568	0.730	1e-119
158286683		471	AGAP006891-PA [Anopheles gambiae str. PE	0.693	0.566	0.724	1e-119
193632011		462	PREDICTED: NADH dehydrogenase [ubiquinon	0.672	0.560	0.738	1e-119
312383663		473	hypothetical protein AND_03103 [Anophele	0.680	0.553	0.723	1e-119
405961731		1645	NADH dehydrogenase [ubiquinone] iron-sul	0.789	0.184	0.573	1e-118
24638644		468	CG1970, isoform A [Drosophila melanogast	0.672	0.553	0.731	1e-118

>gi\|357628760\|gb\|EHJ77963.1\| NADH dehydrogenase-ubiquinone Fe-S protein 2 precursor [Danaus plexippus]	Back alignment and taxonomy information

 Score =  442 bits (1137), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 212/279 (75%), Positives = 238/279 (85%), Gaps = 20/279 (7%)

Query: 51  LFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGV 110
           LFAEITRILNHIMAVGTHALDVGA+TPFFWLFEEREKMMEFYER SGARMHAAY+RPGGV
Sbjct: 176 LFAEITRILNHIMAVGTHALDVGALTPFFWLFEEREKMMEFYERVSGARMHAAYIRPGGV 235

Query: 111 ALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVM 170
           +LD+P+GL+DDIY F S F  RLDEVED+LT NR+W+QRTKDVG+V+A+DALNYGFSGVM
Sbjct: 236 SLDMPLGLMDDIYEFASKFGERLDEVEDVLTTNRIWVQRTKDVGVVTAQDALNYGFSGVM 295

Query: 171 LRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGN-----VIGMKEMRQSLRIVEQAINKMP 225
           LRGSGIKWDLRK QPYD Y+  EFD+PIGT+G+     +I ++EMRQSLRI++Q +N+MP
Sbjct: 296 LRGSGIKWDLRKTQPYDAYDKVEFDVPIGTNGDCYDRYLIRVEEMRQSLRIIDQCLNQMP 355

Query: 226 GGEVRTDDMKISTPSRSEMK---------------GYPVPPGATYTAVEAPKGEFGVYLV 270
            GEV+TDD K++ PSR EMK               GY VPPGATYTAVEAPKGEFGVYLV
Sbjct: 356 PGEVKTDDAKLTPPSREEMKTSMEALIHHFKLFTQGYAVPPGATYTAVEAPKGEFGVYLV 415

Query: 271 SDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII 309
           SDG SKPYRCKIKAPGFAHLAALEKIGK S LADIVAII
Sbjct: 416 SDGGSKPYRCKIKAPGFAHLAALEKIGKNSMLADIVAII 454

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|195402219\|ref\|XP_002059704.1\| GJ13840 [Drosophila virilis] gi\|194155918\|gb\|EDW71102.1\| GJ13840 [Drosophila virilis] gi\|263359639\|gb\|ACY70475.1\| hypothetical protein DVIR88_6g0012 [Drosophila virilis]	Back alignment and taxonomy information

>gi\|114051447\|ref\|NP_001040366.1\| NADH dehydrogenase-ubiquinone Fe-S protein 2 [Bombyx mori] gi\|95102646\|gb\|ABF51261.1\| NADH dehydrogenase-ubiquinone Fe-S protein 2 precursor [Bombyx mori]	Back alignment and taxonomy information

>gi\|170051629\|ref\|XP_001861851.1\| NADH dehydrogenase iron-sulfur protein 2, mitochondrial [Culex quinquefasciatus] gi\|167872807\|gb\|EDS36190.1\| NADH dehydrogenase iron-sulfur protein 2, mitochondrial [Culex quinquefasciatus]	Back alignment and taxonomy information

>gi\|332373630\|gb\|AEE61956.1\| unknown [Dendroctonus ponderosae]	Back alignment and taxonomy information

>gi\|158286683\|ref\|XP_308864.3\| AGAP006891-PA [Anopheles gambiae str. PEST] gi\|157020586\|gb\|EAA03959.4\| AGAP006891-PA [Anopheles gambiae str. PEST]	Back alignment and taxonomy information

>gi\|193632011\|ref\|XP_001947632.1\| PREDICTED: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial-like [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|312383663\|gb\|EFR28661.1\| hypothetical protein AND_03103 [Anopheles darlingi]	Back alignment and taxonomy information

>gi\|405961731\|gb\|EKC27484.1\| NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial [Crassostrea gigas]	Back alignment and taxonomy information

>gi\|24638644\|ref\|NP_651926.1\| CG1970, isoform A [Drosophila melanogaster] gi\|442614419\|ref\|NP_001259064.1\| CG1970, isoform B [Drosophila melanogaster] gi\|22759353\|gb\|AAF59336.2\| CG1970, isoform A [Drosophila melanogaster] gi\|189182170\|gb\|ACD81861.1\| LD47962p [Drosophila melanogaster] gi\|440218151\|gb\|AGB96554.1\| CG1970, isoform B [Drosophila melanogaster]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		385
FB\|FBgn0039909		468	CG1970 [Drosophila melanogaste	0.506	0.416	0.745	9.8e-97
MGI\|MGI:2385112		463	Ndufs2 "NADH dehydrogenase (ub	0.545	0.453	0.675	7.9e-93
RGD\|1307109		463	Ndufs2 "NADH dehydrogenase (ub	0.545	0.453	0.675	1.6e-92
UNIPROTKB\|Q641Y2		463	Ndufs2 "NADH dehydrogenase [ub	0.545	0.453	0.675	1.6e-92
UNIPROTKB\|F1PVM9		463	NDUFS2 "Uncharacterized protei	0.545	0.453	0.662	4.9e-91
UNIPROTKB\|F1S1A8		463	NDUFS2 "Uncharacterized protei	0.545	0.453	0.662	1e-90
UNIPROTKB\|P17694		463	NDUFS2 "NADH dehydrogenase [ub	0.545	0.453	0.662	1.3e-90
UNIPROTKB\|Q0MQG3		463	NDUFS2 "NADH dehydrogenase [ub	0.545	0.453	0.652	1.7e-90
UNIPROTKB\|Q0MQG4		463	NDUFS2 "NADH dehydrogenase [ub	0.545	0.453	0.652	2.1e-90
UNIPROTKB\|Q0MQG5		463	NDUFS2 "NADH dehydrogenase [ub	0.545	0.453	0.652	2.1e-90

FB\|FBgn0039909 CG1970 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 811 (290.5 bits), Expect = 9.8e-97, Sum P(2) = 9.8e-97
 Identities = 149/200 (74%), Positives = 176/200 (88%)

Query:    51 LFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGV 110
             LFAEITRILNHIMAVGTHALDVGA+TPFFWLFEEREKMMEFYER SGARMHAAY+RPGGV
Sbjct:   178 LFAEITRILNHIMAVGTHALDVGALTPFFWLFEEREKMMEFYERVSGARMHAAYIRPGGV 237

Query:   111 ALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVM 170
             +LD+P+GL+DDIY F S F+ RLDEVED+LT NR+W+QRT+D+GIV+AE+ALNYGFSGVM
Sbjct:   238 SLDMPLGLMDDIYEFASKFAERLDEVEDVLTTNRIWVQRTEDIGIVTAEEALNYGFSGVM 297

Query:   171 LRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGN-----VIGMKEMRQSLRIVEQAINKMP 225
             LRGSGIKWDLRK QPYD Y    FD+PIGT G+     +  ++EMRQSLRI++Q +N+MP
Sbjct:   298 LRGSGIKWDLRKQQPYDAYNLVNFDVPIGTKGDCYDRYLCRVEEMRQSLRIIDQCLNQMP 357

Query:   226 GGEVRTDDMKISTPSRSEMK 245
              GE++TDD K++ PSRSEMK
Sbjct:   358 AGEIKTDDAKVAPPSRSEMK 377

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=ISS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISS

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

GO:0006120 "mitochondrial electron transport, NADH to ubiquinone" evidence=ISS

GO:0051287 "NAD binding" evidence=IEA

GO:0048038 "quinone binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0048812 "neuron projection morphogenesis" evidence=IMP

GO:0046331 "lateral inhibition" evidence=IMP

MGI\|MGI:2385112 Ndufs2 "NADH dehydrogenase (ubiquinone) Fe-S protein 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1307109 Ndufs2 "NADH dehydrogenase (ubiquinone) Fe-S protein 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q641Y2 Ndufs2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PVM9 NDUFS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1S1A8 NDUFS2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|P17694 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0MQG3 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Pongo pygmaeus (taxid:9600)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0MQG4 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Gorilla gorilla gorilla (taxid:9595)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0MQG5 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Pan troglodytes (taxid:9598)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q3YS37	NUOD_EHRCJ	1, ., 6, ., 9, 9, ., 5	0.575	0.6753	0.6615	yes	N/A
Q5FGV3	NUOD_EHRRG	1, ., 6, ., 9, 9, ., 5	0.5714	0.6753	0.6615	yes	N/A
Q0MQG5	NDUS2_PANTR	1, ., 6, ., 9, 9, ., 3	0.6576	0.7116	0.5917	yes	N/A
Q2GDJ8	NUOD_NEOSM	1, ., 6, ., 9, 9, ., 5	0.5400	0.6935	0.6881	yes	N/A
A9CJA9	NUOD_AGRT5	1, ., 6, ., 9, 9, ., 5	0.5279	0.6805	0.6616	yes	N/A
A8EZ86	NUOD_RICCK	1, ., 6, ., 9, 9, ., 5	0.5368	0.6883	0.6777	yes	N/A
Q2GGK7	NUOD_EHRCR	1, ., 6, ., 9, 9, ., 5	0.5785	0.6753	0.6615	yes	N/A
O75306	NDUS2_HUMAN	1, ., 6, ., 9, 9, ., 3	0.6576	0.7116	0.5917	yes	N/A
A5CES2	NUOD_ORITB	1, ., 6, ., 9, 9, ., 5	0.5543	0.6883	0.6691	yes	N/A
A7HY46	NUOD_PARL1	1, ., 6, ., 9, 9, ., 5	0.5508	0.6883	0.6760	yes	N/A
A8GN50	NUOD_RICAH	1, ., 6, ., 9, 9, ., 5	0.5438	0.6883	0.6777	yes	N/A
P17694	NDUS2_BOVIN	1, ., 6, ., 9, 9, ., 3	0.6644	0.7116	0.5917	yes	N/A
Q5HB88	NUOD_EHRRW	1, ., 6, ., 9, 9, ., 5	0.575	0.6753	0.6615	yes	N/A
Q5GTF8	NUOD_WOLTR	1, ., 6, ., 9, 9, ., 5	0.5678	0.6753	0.6666	yes	N/A
Q91WD5	NDUS2_MOUSE	1, ., 6, ., 9, 9, ., 3	0.6745	0.7116	0.5917	yes	N/A
Q2RU37	NUOD_RHORT	1, ., 6, ., 9, 9, ., 5	0.5365	0.6935	0.6811	yes	N/A
A8GX80	NUOD_RICB8	1, ., 6, ., 9, 9, ., 5	0.5473	0.6883	0.6777	yes	N/A
A8GRR5	NUOD_RICRS	1, ., 6, ., 9, 9, ., 5	0.5333	0.6883	0.6777	yes	N/A
Q4UM08	NUOD_RICFE	1, ., 6, ., 9, 9, ., 5	0.5508	0.6883	0.6777	yes	N/A
Q1RJI9	NUOD_RICBR	1, ., 6, ., 9, 9, ., 5	0.5473	0.6883	0.6777	yes	N/A
Q23883	NDUS2_DICDI	1, ., 6, ., 9, 9, ., 3	0.5379	0.6961	0.6600	yes	N/A
Q73HJ8	NUOD_WOLPM	1, ., 6, ., 9, 9, ., 5	0.5678	0.6753	0.6666	yes	N/A
Q9ZDH4	NUOD_RICPR	1, ., 6, ., 9, 9, ., 5	0.5473	0.6883	0.6812	yes	N/A
P93306	NDUS2_ARATH	1, ., 6, ., 9, 9, ., 3	0.5614	0.6883	0.6725	yes	N/A
B0ULK7	NUOD_METS4	1, ., 6, ., 9, 9, ., 5	0.5406	0.6727	0.6540	yes	N/A
A8F1C5	NUOD_RICM5	1, ., 6, ., 9, 9, ., 5	0.5403	0.6883	0.6777	yes	N/A
Q4FM88	NUOD_PELUB	1, ., 6, ., 9, 9, ., 5	0.5228	0.6883	0.6777	yes	N/A
Q68X19	NUOD_RICTY	1, ., 6, ., 9, 9, ., 5	0.5403	0.6883	0.6812	yes	N/A
B6ISX8	NUOD_RHOCS	1, ., 6, ., 9, 9, ., 5	0.5563	0.6805	0.6582	yes	N/A
Q92ID8	NUOD_RICCN	1, ., 6, ., 9, 9, ., 5	0.5368	0.6883	0.6777	yes	N/A
Q163Q5	NUOD_ROSDO	1, ., 6, ., 9, 9, ., 5	0.5403	0.6805	0.6437	yes	N/A
Q2W3I7	NUOD_MAGSA	1, ., 6, ., 9, 9, ., 5	0.5483	0.6727	0.6607	yes	N/A
Q2GJY9	NUOD_ANAPZ	1, ., 6, ., 9, 9, ., 5	0.5285	0.6753	0.6582	yes	N/A
B3CSH1	NUOD_ORITI	1, ., 6, ., 9, 9, ., 5	0.5543	0.6883	0.6691	yes	N/A
Q5PAR3	NUOD_ANAMM	1, ., 6, ., 9, 9, ., 5	0.5331	0.6935	0.6708	yes	N/A
B3CLH1	NUOD_WOLPP	1, ., 6, ., 9, 9, ., 5	0.575	0.6753	0.6666	yes	N/A
B0BX71	NUOD_RICRO	1, ., 6, ., 9, 9, ., 5	0.5333	0.6883	0.6777	yes	N/A
Q641Y2	NDUS2_RAT	1, ., 6, ., 9, 9, ., 3	0.6745	0.7116	0.5917	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	1.6.99	0.921

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		385
PRK06075		392	PRK06075, PRK06075, NADH dehydrogenase subunit D;	1e-144
COG0649		398	COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 k	1e-132
TIGR01962		386	TIGR01962, NuoD, NADH dehydrogenase I, D subunit	1e-123
pfam00346		272	pfam00346, Complex1_49kDa, Respiratory-chain NADH	1e-122
PRK12322		366	PRK12322, PRK12322, NADH dehydrogenase subunit D;	8e-86
PRK13292		788	PRK13292, PRK13292, trifunctional NADH dehydrogena	2e-82
PRK11742		575	PRK11742, PRK11742, bifunctional NADH:ubiquinone o	1e-75
PRK07415		394	PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase	4e-71
CHL00017		393	CHL00017, ndhH, NADH dehydrogenase subunit 7	2e-66
COG3261		382	COG3261, HycE, Ni,Fe-hydrogenase III large subunit	6e-43
PRK06075		392	PRK06075, PRK06075, NADH dehydrogenase subunit D;	1e-39
COG0649		398	COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 k	2e-34
TIGR01962		386	TIGR01962, NuoD, NADH dehydrogenase I, D subunit	2e-31
PRK12322		366	PRK12322, PRK12322, NADH dehydrogenase subunit D;	4e-21
PRK11742		575	PRK11742, PRK11742, bifunctional NADH:ubiquinone o	2e-15
PRK13292		788	PRK13292, PRK13292, trifunctional NADH dehydrogena	7e-14
PRK07415		394	PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase	2e-13
CHL00017		393	CHL00017, ndhH, NADH dehydrogenase subunit 7	8e-13
COG3261		382	COG3261, HycE, Ni,Fe-hydrogenase III large subunit	2e-08
PRK06075		392	PRK06075, PRK06075, NADH dehydrogenase subunit D;	9e-07
COG0649		398	COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 k	2e-05
TIGR01962		386	TIGR01962, NuoD, NADH dehydrogenase I, D subunit	1e-04
PRK07415		394	PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase	0.004
cd03577		116	cd03577, NTR_TIMP_like, NTR domain, TIMP-like subf	0.004

>gnl\|CDD\|180385 PRK06075, PRK06075, NADH dehydrogenase subunit D; Validated	Back alignment and domain information

 Score =  414 bits (1067), Expect = e-144
 Identities = 152/281 (54%), Positives = 200/281 (71%), Gaps = 22/281 (7%)

Query: 51  LFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGV 110
           LF E+ RIL+H++ +GTHALD+GAMT F W F EREK+++ YE  +GARMH AY+RPGGV
Sbjct: 100 LFLELNRILSHLLWLGTHALDLGAMTVFLWGFREREKLLDLYEAVTGARMHHAYIRPGGV 159

Query: 111 ALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVM 170
             D+P GLL+DI  F+  F  RLD+ E +LT+NR+W QR   VG+VS E AL  GF+G M
Sbjct: 160 RRDLPDGLLEDIRDFLDYFPKRLDDYETLLTDNRIWKQRLVGVGVVSKERALALGFTGPM 219

Query: 171 LRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGN-----VIGMKEMRQSLRIVEQAINKM- 224
           LR SG+ WDLRK QPY+ Y+  +FD+P+G +G+     ++ ++EMRQSLRI+EQ ++++ 
Sbjct: 220 LRASGVAWDLRKSQPYEVYDELDFDVPVGKNGDCYDRYLVRVEEMRQSLRIIEQCLDRLR 279

Query: 225 -PGGEVRTDDMKISTPSRSEMK---------------GYPVPPGATYTAVEAPKGEFGVY 268
            P G V  DD KI+ P+R EMK               G+ VP G  Y AVE+PKGEFGVY
Sbjct: 280 PPPGPVMVDDPKIAPPARLEMKTSMEALIHHFKLVTEGFRVPAGEVYAAVESPKGEFGVY 339

Query: 269 LVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII 309
           LVSDG +KPYR KI+AP FAHL AL+++ +G  LAD+VAII
Sbjct: 340 LVSDGGNKPYRVKIRAPSFAHLQALDEMCRGHMLADVVAII 380

Length = 392

>gnl\|CDD\|223722 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|233658 TIGR01962, NuoD, NADH dehydrogenase I, D subunit	Back alignment and domain information

>gnl\|CDD\|215871 pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit	Back alignment and domain information

>gnl\|CDD\|183437 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provisional	Back alignment and domain information

>gnl\|CDD\|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit B/C/D; Provisional	Back alignment and domain information

>gnl\|CDD\|236965 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional	Back alignment and domain information

>gnl\|CDD\|180969 PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase subunit H; Validated	Back alignment and domain information

>gnl\|CDD\|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7	Back alignment and domain information

>gnl\|CDD\|225800 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|180385 PRK06075, PRK06075, NADH dehydrogenase subunit D; Validated	Back alignment and domain information

>gnl\|CDD\|223722 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|233658 TIGR01962, NuoD, NADH dehydrogenase I, D subunit	Back alignment and domain information

>gnl\|CDD\|183437 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provisional	Back alignment and domain information

>gnl\|CDD\|236965 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional	Back alignment and domain information

>gnl\|CDD\|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit B/C/D; Provisional	Back alignment and domain information

>gnl\|CDD\|180969 PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase subunit H; Validated	Back alignment and domain information

>gnl\|CDD\|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7	Back alignment and domain information

>gnl\|CDD\|225800 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|180385 PRK06075, PRK06075, NADH dehydrogenase subunit D; Validated	Back alignment and domain information

>gnl\|CDD\|223722 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|233658 TIGR01962, NuoD, NADH dehydrogenase I, D subunit	Back alignment and domain information

>gnl\|CDD\|180969 PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase subunit H; Validated	Back alignment and domain information

>gnl\|CDD\|239632 cd03577, NTR_TIMP_like, NTR domain, TIMP-like subfamily; TIMPs, or tissue inibitors of metalloproteases, are essential regulators of extracellular matrix turnover and remodeling	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		385
COG0649		398	NuoD NADH:ubiquinone oxidoreductase 49 kD subunit	100.0
CHL00017		393	ndhH NADH dehydrogenase subunit 7	100.0
PRK07415		394	NAD(P)H-quinone oxidoreductase subunit H; Validate	100.0
KOG2870\|consensus		452		100.0
PRK12322		366	NADH dehydrogenase subunit D; Provisional	100.0
PRK06075		392	NADH dehydrogenase subunit D; Validated	100.0
TIGR01962		386	NuoD NADH dehydrogenase I, D subunit. This model r	100.0
PRK11742		575	bifunctional NADH:ubiquinone oxidoreductase subuni	100.0
PRK13292		788	trifunctional NADH dehydrogenase I subunit B/C/D;	100.0
COG3261		382	HycE Ni,Fe-hydrogenase III large subunit [Energy p	100.0
PF00346		272	Complex1_49kDa: Respiratory-chain NADH dehydrogena	100.0
TIGR03295		411	frhA coenzyme F420 hydrogenase, subunit alpha. Thi	100.0
COG3259		441	FrhA Coenzyme F420-reducing hydrogenase, alpha sub	100.0
PRK10467		567	hydrogenase 2 large subunit; Provisional	99.94
PF00374		507	NiFeSe_Hases: Nickel-dependent hydrogenase; InterP	99.93
COG3261		382	HycE Ni,Fe-hydrogenase III large subunit [Energy p	99.91
PRK12322		366	NADH dehydrogenase subunit D; Provisional	99.91
CHL00017		393	ndhH NADH dehydrogenase subunit 7	99.91
PRK10170		597	hydrogenase 1 large subunit; Provisional	99.91
COG0649		398	NuoD NADH:ubiquinone oxidoreductase 49 kD subunit	99.9
TIGR01962		386	NuoD NADH dehydrogenase I, D subunit. This model r	99.89
PRK13292		788	trifunctional NADH dehydrogenase I subunit B/C/D;	99.89
PRK06075		392	NADH dehydrogenase subunit D; Validated	99.89
PRK07415		394	NAD(P)H-quinone oxidoreductase subunit H; Validate	99.89
PRK11742		575	bifunctional NADH:ubiquinone oxidoreductase subuni	99.88
PRK10170		597	hydrogenase 1 large subunit; Provisional	99.8
KOG2870\|consensus		452		99.8
PRK10467		567	hydrogenase 2 large subunit; Provisional	99.77
TIGR03295		411	frhA coenzyme F420 hydrogenase, subunit alpha. Thi	99.77
COG0374		545	HyaB Ni,Fe-hydrogenase I large subunit [Energy pro	99.76
PF00374		507	NiFeSe_Hases: Nickel-dependent hydrogenase; InterP	99.72
COG0374		545	HyaB Ni,Fe-hydrogenase I large subunit [Energy pro	99.67
COG3259		441	FrhA Coenzyme F420-reducing hydrogenase, alpha sub	99.53

>COG0649 NuoD NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

Probab=100.00  E-value=1.4e-72  Score=543.86  Aligned_cols=289  Identities=49%  Similarity=0.910  Sum_probs=274.6

Q ss_pred             hhhhhhhhcCCCC-hhHHHHHHHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHHHHHHHHHHHccCCccCCCeeeC
Q psy7154          30 QIRNMVINFGPQH-PAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPG  108 (385)
Q Consensus        30 ~~~~~~~~~g~~~-p~a~~lR~ll~EleRI~sHll~l~~l~~d~G~~~~~~~~~~~RE~~~~l~e~l~G~R~h~~~~~pG  108 (385)
                      =..|+++..|.+. ++|+.||++++|+.||+|||+|+|.++.|+|+.|+++|+|+.||++++++|.+||.|+|++|.+||
T Consensus        86 y~~AvEkLlgieVPeRAq~IRvm~~EL~RI~sHLl~lg~~~~dlGa~T~f~yaf~eRE~i~~l~E~~tGaRm~~~y~rpG  165 (398)
T COG0649          86 YVLAVEKLLGIEVPERAQYIRVMLSELNRIASHLLWLGTFALDLGAMTPFLYAFREREKIMDLFEAITGARMHHAYFRPG  165 (398)
T ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccHhhhhhHHHHHHHHHHHHHhcccccccccccC
Confidence            3678999999998 699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCChhHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHhhccccccChhhHhhhcccCcccccCCcccccccccCCCC
Q psy7154         109 GVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDG  188 (385)
Q Consensus       109 Gv~~dl~~~~~~~i~~~l~~~~~~~~e~~~~~~~~~~~~~R~~~vG~l~~~~a~~~~~~Gp~~RasGv~~D~R~~~py~~  188 (385)
                      ||++|+|+++.+.+.++++++++.++++.+++.+|++|+.|++++|++|+++|.+||+|||.+||||++||+||+.||..
T Consensus       166 GV~~DlP~~~~e~i~~f~d~~~~~l~eye~l~~~N~I~~~R~~gVGv~s~e~A~~~G~tGp~lR~SGv~~DvRK~~PY~~  245 (398)
T COG0649         166 GVRRDLPEGWLELIREFLDYFPKRLDEYEKLLTKNRIWRARLEGVGVLSKEEALEWGVTGPMLRASGVDYDVRKDEPYEA  245 (398)
T ss_pred             cccccCCHHHHHHHHHHHHHHHHhHHHHHHHHhcChHHHHhcccceeecHHHHHHhCCcCccccccCCcchhcccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccccCCCCcc-----hHHHHHHHHHHHHHHHHHcCCCCCccccCCcCCCCcccccC---------------CCC
Q psy7154         189 YENFEFDIPIGTHGNV-----IGMKEMRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSEMK---------------GYP  248 (385)
Q Consensus       189 Y~~~~f~~~~~~~GD~-----vR~~Ei~~Si~ii~q~L~~l~~g~~~~~~~~~~~p~~~~~~---------------~~~  248 (385)
                      |++++|++|+++.|||     ||++||.||++||+||+++||.||+...+.+..+|++..++               ++.
T Consensus       246 Yd~~dFdVpv~~~GD~yaR~lvR~~EmrqS~rIIeQcl~~l~~gP~~~~~~~~~~p~~~~~~~~~e~li~~f~l~~~g~~  325 (398)
T COG0649         246 YDELDFDVPVGKNGDCYARYLVRMEEMRQSIRIIEQCLDKLPKGPVKNEDPKTTPPSKERMKESMEALIHHFKLVTEGFK  325 (398)
T ss_pred             ccccceeccccCCCchhhhhhhhHHHHHHHHHHHHHHHHhCcCCCCcccccccCCCchHHhhhhHHHHhhheeeeccccc
Confidence            9999999999999999     99999999999999999999999988776665556433221               677


Q ss_pred             CCCCceEEeecCCCCcccEEEEEcCCCCeeEEEEeCCCcccHHHHHHhhcCCcccccccc---cccccccchh
Q psy7154         249 VPPGATYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAI---IDPHIGLLHR  318 (385)
Q Consensus       249 ~~~Geg~g~vEapRG~l~h~~~~dg~g~~~r~~ir~Ps~~n~~al~~~l~G~~i~D~V~~---~dp~ig~~hR  318 (385)
                      +|+||.|+.||||||++++|+++||+.+|||++||+|||.|+++|+.+++|+.++|.+++   +|++.|...|
T Consensus       326 vP~GE~y~~vE~~kGE~g~yv~SDG~~kPYR~kiR~Psf~~L~~~~~~~~G~~~AD~~ailGS~D~v~gEvDR  398 (398)
T COG0649         326 VPAGEVYAAVEAPKGELGVYIVSDGSNKPYRVKIRAPSFAHLQALPELLKGHRLADLIAILGSIDIVMGEVDR  398 (398)
T ss_pred             CCCCceEEeeecCCccEEEEEEeCCCCCceeEEecCCChhHHHHHHHHhCCCchHHHHHHHhccCccCCCCCC
Confidence            899999999999999999999999999999999999999999999999999999999874   8999998765

>CHL00017 ndhH NADH dehydrogenase subunit 7	Back alignment and domain information

>PRK07415 NAD(P)H-quinone oxidoreductase subunit H; Validated	Back alignment and domain information

>KOG2870\|consensus	Back alignment and domain information

>PRK12322 NADH dehydrogenase subunit D; Provisional	Back alignment and domain information

>PRK06075 NADH dehydrogenase subunit D; Validated	Back alignment and domain information

>TIGR01962 NuoD NADH dehydrogenase I, D subunit	Back alignment and domain information

>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional	Back alignment and domain information

>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional	Back alignment and domain information

>COG3261 HycE Ni,Fe-hydrogenase III large subunit [Energy production and conversion]	Back alignment and domain information

>PF00346 Complex1_49kDa: Respiratory-chain NADH dehydrogenase, 49 Kd subunit; InterPro: IPR001135 This entry represents subunit D (NuoD) of NADH-quinone oxidoreductase (1	Back alignment and domain information

>TIGR03295 frhA coenzyme F420 hydrogenase, subunit alpha	Back alignment and domain information

>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]	Back alignment and domain information

>PRK10467 hydrogenase 2 large subunit; Provisional	Back alignment and domain information

>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes	Back alignment and domain information

>COG3261 HycE Ni,Fe-hydrogenase III large subunit [Energy production and conversion]	Back alignment and domain information

>PRK12322 NADH dehydrogenase subunit D; Provisional	Back alignment and domain information

>CHL00017 ndhH NADH dehydrogenase subunit 7	Back alignment and domain information

>PRK10170 hydrogenase 1 large subunit; Provisional	Back alignment and domain information

>COG0649 NuoD NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

>TIGR01962 NuoD NADH dehydrogenase I, D subunit	Back alignment and domain information

>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional	Back alignment and domain information

>PRK06075 NADH dehydrogenase subunit D; Validated	Back alignment and domain information

>PRK07415 NAD(P)H-quinone oxidoreductase subunit H; Validated	Back alignment and domain information

>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional	Back alignment and domain information

>PRK10170 hydrogenase 1 large subunit; Provisional	Back alignment and domain information

>KOG2870\|consensus	Back alignment and domain information

>PRK10467 hydrogenase 2 large subunit; Provisional	Back alignment and domain information

>TIGR03295 frhA coenzyme F420 hydrogenase, subunit alpha	Back alignment and domain information

>COG0374 HyaB Ni,Fe-hydrogenase I large subunit [Energy production and conversion]	Back alignment and domain information

>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes	Back alignment and domain information

>COG0374 HyaB Ni,Fe-hydrogenase I large subunit [Energy production and conversion]	Back alignment and domain information

>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		385
2fug_4		409	Crystal Structure Of The Hydrophilic Domain Of Resp		1e-56
2fug_4		409	Crystal Structure Of The Hydrophilic Domain Of Resp		2e-11

>pdb|2FUG|4 Chain 4, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 409

Back alignment and structure

Iteration: 1

Score = 217 bits (552), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 107/299 (35%), Positives = 178/299 (59%), Gaps = 23/299 (7%) Query: 43 PAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHA 102 P A + ++ E++R+ +H++ +GT LD+GA+TPFF+ F ERE +++ +E +G R H Sbjct: 111 PRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHH 170 Query: 103 AYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDAL 162 Y+R GGV D+P + ++ + R+DE E + E+ ++ +R + VG++ E A+ Sbjct: 171 NYIRIGGVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAI 230 Query: 163 NYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNV-----IGMKEMRQSLRIV 217 + G +G LR SG+ +D+RK PY GYE + FD+P+G G+V + ++EMR+S++I+ Sbjct: 231 DLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKII 290 Query: 218 EQAINKMPGGEVRTDDMKISTPSRSEM---------------KGYPVPPGATYTAVEAPK 262 +QA+ ++ G VR + +I+ P R + +G+ P G Y E+ + Sbjct: 291 KQALERLEPGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESAR 350 Query: 263 GEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII---DPHIGLLHR 318 GE G Y+VSDG S PYR K++AP F +L +L KG + D+VAII DP +G + R Sbjct: 351 GELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 409

PyMOL of 2fug

>pdb|2FUG|4 Chain 4, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 409

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		385
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	1e-163
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	2e-41
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	1e-07

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4* Length = 409	Back alignment and structure

 Score =  463 bits (1194), Expect = e-163
 Identities = 101/279 (36%), Positives = 168/279 (60%), Gaps = 20/279 (7%)

Query: 51  LFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGGV 110
           +  E++R+ +H++ +GT  LD+GA+TPFF+ F ERE +++ +E  +G R H  Y+R GGV
Sbjct: 119 ILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGV 178

Query: 111 ALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVM 170
             D+P   + ++   +     R+DE E +  E+ ++ +R + VG++  E A++ G +G  
Sbjct: 179 KEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGS 238

Query: 171 LRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNV-----IGMKEMRQSLRIVEQAINKMP 225
           LR SG+ +D+RK  PY GYE + FD+P+G  G+V     + ++EMR+S++I++QA+ ++ 
Sbjct: 239 LRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLE 298

Query: 226 GGEVRTDDMKISTPSRSEMK---------------GYPVPPGATYTAVEAPKGEFGVYLV 270
            G VR  + +I+ P R  ++               G+  P G  Y   E+ +GE G Y+V
Sbjct: 299 PGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIV 358

Query: 271 SDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII 309
           SDG S PYR K++AP F +L +L    KG  + D+VAII
Sbjct: 359 SDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAII 397

PyMOL of 3i9v

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4* Length = 409	Back alignment and structure

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4* Length = 409	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		385
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	100.0
2wpn_B		495	Periplasmic [nifese] hydrogenase, large subunit, s	100.0
1yqw_Q		549	Periplasmic [NIFE] hydrogenase large subunit; NI-F	100.0
1wui_L		534	Periplasmic [NIFE] hydrogenase large subunit; high	100.0
1cc1_L		498	Hydrogenase (large subunit); NI-Fe-Se hydrogenase,	100.0
1e3d_B		542	[NIFE] hydrogenase large subunit; molecular modell	100.0
3ayx_A		596	Membrane-bound hydrogenase large subunit; oxidored	100.0
1yq9_H		536	Periplasmic [NIFE] hydrogenase large subunit; oxid	100.0
3myr_B		561	Nickel-dependent hydrogenase large subunit; [NIFE]	99.93
3uqy_L		582	Hydrogenase-1 large chain; membrane-bound hydrogen	99.91
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	99.89
3uqy_L		582	Hydrogenase-1 large chain; membrane-bound hydrogen	99.87
1wui_L		534	Periplasmic [NIFE] hydrogenase large subunit; high	99.85
1e3d_B		542	[NIFE] hydrogenase large subunit; molecular modell	99.85
1yqw_Q		549	Periplasmic [NIFE] hydrogenase large subunit; NI-F	99.85
1cc1_L		498	Hydrogenase (large subunit); NI-Fe-Se hydrogenase,	99.85
2wpn_B		495	Periplasmic [nifese] hydrogenase, large subunit, s	99.85
3ayx_A		596	Membrane-bound hydrogenase large subunit; oxidored	99.85
3myr_B		561	Nickel-dependent hydrogenase large subunit; [NIFE]	99.85
1yq9_H		536	Periplasmic [NIFE] hydrogenase large subunit; oxid	99.84
3i9v_5		207	NADH-quinone oxidoreductase subunit 5; electron tr	89.34

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4*	Back alignment and structure

Probab=100.00  E-value=7.6e-70  Score=544.55  Aligned_cols=289  Identities=37%  Similarity=0.766  Sum_probs=273.9

Q ss_pred             hhhhhhhhcCCCC-hhHHHHHHHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHHHHHHHHHHHccCCccCCCeeeC
Q psy7154          30 QIRNMVINFGPQH-PAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPG  108 (385)
Q Consensus        30 ~~~~~~~~~g~~~-p~a~~lR~ll~EleRI~sHll~l~~l~~d~G~~~~~~~~~~~RE~~~~l~e~l~G~R~h~~~~~pG  108 (385)
                      =.+|+++.+|+++ |+|+.+|+|++|+|||+||++|++.++.|+|+.++++|++++||.++++++.+||+|+|+++++||
T Consensus        97 ~~~AvE~~~gievP~ra~~iR~l~~eleRI~sHll~lg~~a~d~G~~t~~~~~~~~RE~~~~i~e~~~G~R~h~~~~~pG  176 (409)
T 3i9v_4           97 YALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIG  176 (409)
T ss_dssp             HHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHSSSSSCCCBCSS
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHHHHHHHHcCCccccCceeeC
Confidence            3689999999988 899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCChhHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHhhccccccChhhHhhhcccCcccccCCcccccccccCCCC
Q psy7154         109 GVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDG  188 (385)
Q Consensus       109 Gv~~dl~~~~~~~i~~~l~~~~~~~~e~~~~~~~~~~~~~R~~~vG~l~~~~a~~~~~~Gp~~RasGv~~D~R~~~py~~  188 (385)
                      ||++|++++++++++++++.+++.++++.+++.+|++|.+|++++|+++.++|.+||++||++||||+++|+|++.||+.
T Consensus       177 Gv~~dl~~~~~~~i~~~l~~~~~~~~e~~~l~~~n~i~~~R~~gvGvl~~e~A~~~g~tGp~~RaSGv~~D~R~~~PY~~  256 (409)
T 3i9v_4          177 GVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSG  256 (409)
T ss_dssp             BBSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHSCTTHHHHHSSSSCBCHHHHHHHTCCSSSSGGGTCCCCHHHHSCCSS
T ss_pred             CeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHhhcCCccccCHHHHHHhCCcCcccccCCCccchhhcCcchh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccccCCCCcc-----hHHHHHHHHHHHHHHHHHcCCCCCccccCCcCCCCccccc---------------CCCC
Q psy7154         189 YENFEFDIPIGTHGNV-----IGMKEMRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSEM---------------KGYP  248 (385)
Q Consensus       189 Y~~~~f~~~~~~~GD~-----vR~~Ei~~Si~ii~q~L~~l~~g~~~~~~~~~~~p~~~~~---------------~~~~  248 (385)
                      |++++|++|+.+.|||     ||+.||.||++||+|||++||+|++..+.++..+|.+..+               .+++
T Consensus       257 Y~~~~f~v~~~~~GD~~aR~~VR~~E~~qSl~ii~q~l~~lp~G~~~~~~~~~~~p~~~~~~~~~e~li~hf~~~~~~~~  336 (409)
T 3i9v_4          257 YETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFH  336 (409)
T ss_dssp             GGGSCCCCCCCSSBCHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCCBCCCTTTSCCCGGGGGTCHHHHHHHHHHHHSCCC
T ss_pred             hccCCCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcccccccccCCchhhhhcchHHhhhhhhccccccc
Confidence            9999999999999999     9999999999999999999999998877655444543332               2567


Q ss_pred             CCCCceEEeecCCCCcccEEEEEcCCCCeeEEEEeCCCcccHHHHHHhhcCCccccccc---ccccccccchh
Q psy7154         249 VPPGATYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVA---IIDPHIGLLHR  318 (385)
Q Consensus       249 ~~~Geg~g~vEapRG~l~h~~~~dg~g~~~r~~ir~Ps~~n~~al~~~l~G~~i~D~V~---~~dp~ig~~hR  318 (385)
                      +|+|++|+.||||||+++||+++||+++|+|++||+|||+||++|+.+++|+.++|+++   ++|||+||..|
T Consensus       337 ~p~Ge~~~~vEapRGe~~~~~~sdg~~~p~R~kir~Psf~nl~~l~~~~~G~~iaD~~~i~~S~D~~~~e~DR  409 (409)
T 3i9v_4          337 PPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR  409 (409)
T ss_dssp             CCSEEEECCEEETTEEEEEEEEECSSSSCSEEEEECHHHHTTTTTTTTTSSSCSGGGTHHHHTTCCCHHHHHC
T ss_pred             CCCceEEEEEEcCCcEEEEEEEECCCCcEEEEEEECCChHHHHHHHHHHCCCcchHHHHHHhCcCCCcccccC
Confidence            89999999999999999999999999999999999999999999999999999999986   49999999876

PyMOL of 3i9v

>2wpn_B Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris}	Back alignment and structure

>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L	Back alignment and structure

>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.18.1.1 PDB: 1ubj_L 1ubh_L 1ubl_L 1ubm_L 1ubo_L 1ubr_L 1ubt_L 1ubu_L 1wuh_L* 1ubk_L* 1wuj_L 1wuk_L 1wul_L 1h2r_L 1h2a_L	Back alignment and structure

>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1	Back alignment and structure

>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} SCOP: e.18.1.1	Back alignment and structure

>3ayx_A Membrane-bound hydrogenase large subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_A 3ayz_A 3rgw_L	Back alignment and structure

>1yq9_H Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.18.1.1 PDB: 2frv_L 1frv_B	Back alignment and structure

>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} SCOP: e.18.1.0	Back alignment and structure

>3uqy_L Hydrogenase-1 large chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_L* 3use_L*	Back alignment and structure

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4*	Back alignment and structure

>3uqy_L Hydrogenase-1 large chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_L* 3use_L*	Back alignment and structure

>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.18.1.1 PDB: 1ubj_L 1ubh_L 1ubl_L 1ubm_L 1ubo_L 1ubr_L 1ubt_L 1ubu_L 1wuh_L* 1ubk_L* 1wuj_L 1wuk_L 1wul_L 1h2r_L 1h2a_L	Back alignment and structure

>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} SCOP: e.18.1.1	Back alignment and structure

>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L	Back alignment and structure

>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1	Back alignment and structure

>2wpn_B Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris}	Back alignment and structure

>3ayx_A Membrane-bound hydrogenase large subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_A 3ayz_A 3rgw_L	Back alignment and structure

>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} SCOP: e.18.1.0	Back alignment and structure

>1yq9_H Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.18.1.1 PDB: 2frv_L 1frv_B	Back alignment and structure

>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_5* 2fug_5* 3iam_5* 3ias_5* 3m9s_5*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		385
d2fug41		375	e.18.1.2 (4:35-409) NADH-quinone oxidoreductase ch	2e-65
d2fug41		375	e.18.1.2 (4:35-409) NADH-quinone oxidoreductase ch	5e-25
d1cc1l_		487	e.18.1.1 (L:) Nickel-iron hydrogenase, large subun	1e-22
d1cc1l_		487	e.18.1.1 (L:) Nickel-iron hydrogenase, large subun	5e-16
d1e3db_		537	e.18.1.1 (B:) Nickel-iron hydrogenase, large subun	4e-19
d1e3db_		537	e.18.1.1 (B:) Nickel-iron hydrogenase, large subun	7e-17
d1yq9h1		530	e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large	6e-18
d1yq9h1		530	e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large	2e-16
d1wuil1		534	e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large	9e-18
d1wuil1		534	e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large	4e-17
d1frfl_		543	e.18.1.1 (L:) Nickel-iron hydrogenase, large subun	7e-17
d1frfl_		543	e.18.1.1 (L:) Nickel-iron hydrogenase, large subun	1e-13

>d2fug41 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus thermophilus [TaxId: 274]} Length = 375	Back information, alignment and structure


class: Multi-domain proteins (alpha and beta)
fold: HydB/Nqo4-like
superfamily: HydB/Nqo4-like
family: Nqo4-like
domain: NADH-quinone oxidoreductase chain 4, Nqo4
species: Thermus thermophilus [TaxId: 274]

 Score =  210 bits (536), Expect = 2e-65
 Identities = 106/296 (35%), Positives = 176/296 (59%), Gaps = 23/296 (7%)

Query: 42  HPAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMH 101
            P A  + ++  E++R+ +H++ +GT  LD+GA+TPFF+ F ERE +++ +E  +G R H
Sbjct: 76  PPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFH 135

Query: 102 AAYVRPGGVALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDA 161
             Y+R GGV  D+P   + ++   +     R+DE E +  E+ ++ +R + VG++  E A
Sbjct: 136 HNYIRIGGVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVA 195

Query: 162 LNYGFSGVMLRGSGIKWDLRKVQPYDGYENFEFDIPIGTHGNV-----IGMKEMRQSLRI 216
           ++ G +G  LR SG+ +D+RK  PY GYE + FD+P+G  G+V     + ++EMR+S++I
Sbjct: 196 IDLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKI 255

Query: 217 VEQAINKMPGGEVRTDDMKISTPSRSEMK---------------GYPVPPGATYTAVEAP 261
           ++QA+ ++  G VR  + +I+ P R  ++               G+  P G  Y   E+ 
Sbjct: 256 IKQALERLEPGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESA 315

Query: 262 KGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADIVAII---DPHIG 314
           +GE G Y+VSDG S PYR K++AP F +L +L    KG  + D+VAII   DP +G
Sbjct: 316 RGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMG 371

PyMOL of d2fug41

>d2fug41 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus thermophilus [TaxId: 274]} Length = 375	Back information, alignment and structure

>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 487	Back information, alignment and structure

>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 487	Back information, alignment and structure

>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]} Length = 537	Back information, alignment and structure

>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]} Length = 537	Back information, alignment and structure

>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]} Length = 530	Back information, alignment and structure

>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]} Length = 530	Back information, alignment and structure

>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 534	Back information, alignment and structure

>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 534	Back information, alignment and structure

>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 543	Back information, alignment and structure

>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 543	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		385
d2fug41		375	NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus	100.0
d1wuil1		534	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d1cc1l_		487	Nickel-iron hydrogenase, large subunit {Desulfomic	100.0
d1yq9h1		530	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d1e3db_		537	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d1frfl_		543	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d2fug41		375	NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus	99.88
d1yq9h1		530	Nickel-iron hydrogenase, large subunit {Desulfovib	99.83
d1wuil1		534	Nickel-iron hydrogenase, large subunit {Desulfovib	99.83
d1frfl_		543	Nickel-iron hydrogenase, large subunit {Desulfovib	99.83
d1e3db_		537	Nickel-iron hydrogenase, large subunit {Desulfovib	99.83
d1cc1l_		487	Nickel-iron hydrogenase, large subunit {Desulfomic	99.82

>d2fug41 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: HydB/Nqo4-like
superfamily: HydB/Nqo4-like
family: Nqo4-like
domain: NADH-quinone oxidoreductase chain 4, Nqo4
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=2.5e-50  Score=398.17  Aligned_cols=288  Identities=36%  Similarity=0.767  Sum_probs=257.5

Q ss_pred             hhhhhhhcCCCC-hhHHHHHHHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHHHHHHHHHHHccCCccCCCeeeCc
Q psy7154          31 IRNMVINFGPQH-PAAHGVLLLFAEITRILNHIMAVGTHALDVGAMTPFFWLFEEREKMMEFYERASGARMHAAYVRPGG  109 (385)
Q Consensus        31 ~~~~~~~~g~~~-p~a~~lR~ll~EleRI~sHll~l~~l~~d~G~~~~~~~~~~~RE~~~~l~e~l~G~R~h~~~~~pGG  109 (385)
                      .+|+|++||+.+ |.++++|.|++|+||||||++|++.++.+.++.+++++++++|+.++++++.++|+|+|+++++|||
T Consensus        64 ~~AlE~a~gv~~p~~a~~lR~l~~~~e~i~sH~l~~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~~G~~~h~~~~~~gG  143 (375)
T d2fug41          64 ALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGG  143 (375)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHTSSSSSCCCEETTE
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHHHHHHhHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHhcCceeeecceeccc
Confidence            689999999999 8999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCChhHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHhhccccccChhhHhhhcccCcccccCCcccccccccCCCCc
Q psy7154         110 VALDIPIGLLDDIYHFISTFSARLDEVEDMLTENRLWIQRTKDVGIVSAEDALNYGFSGVMLRGSGIKWDLRKVQPYDGY  189 (385)
Q Consensus       110 v~~dl~~~~~~~i~~~l~~~~~~~~e~~~~~~~~~~~~~R~~~vG~l~~~~a~~~~~~Gp~~RasGv~~D~R~~~py~~Y  189 (385)
                      ++++++.+.++.++..++.+++.+.+..+++.+++.+..|+.++|.++...+.++|.+||.+|++|++.|.|+..||..|
T Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  223 (375)
T d2fug41         144 VKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGY  223 (375)
T ss_dssp             ESSCCCTTHHHHHHHHTTTTTTTTHHHHHHHSSCSCCTTSCSCCCCSSSCSTTTTTTCCSSCCSSCCTTTTTCCSSCCCC
T ss_pred             eeeCCChHHHHHHHHHHHhhHHHHHHHHHhhccCcccccccCCcccccchhhhhcCcccccccccccccccccccCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccccCCCCcc-----hHHHHHHHHHHHHHHHHHcCCCCCccccCCcCCCCcccc---------------cCCCCC
Q psy7154         190 ENFEFDIPIGTHGNV-----IGMKEMRQSLRIVEQAINKMPGGEVRTDDMKISTPSRSE---------------MKGYPV  249 (385)
Q Consensus       190 ~~~~f~~~~~~~GD~-----vR~~Ei~~Si~ii~q~L~~l~~g~~~~~~~~~~~p~~~~---------------~~~~~~  249 (385)
                      +..+|+.++.+.||+     +|+.|+.+|.+++++++.+.+.+................               ..++++
T Consensus       224 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  303 (375)
T d2fug41         224 ETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHP  303 (375)
T ss_dssp             -----CCCCCCSSSSHHHHHHHHHHHHHHHHHHHHHHHSCCCSCCBCCCTTTSCCCTTCTTTCTTHHHHHHHHHHSCCCC
T ss_pred             cccccccccccCCcccccchhhhhhhhcchHHHHHHHHhCCCCCccccchhhcchhHHHHHhhhhhhhccccccccCCcC
Confidence            999999999999999     999999999999999999988765433211110000000               014567


Q ss_pred             CCCceEEeecCCCCcccEEEEEcCCCCeeEEEEeCCCcccHHHHHHhhcCCccccc---ccccccccccchh
Q psy7154         250 PPGATYTAVEAPKGEFGVYLVSDGTSKPYRCKIKAPGFAHLAALEKIGKGSFLADI---VAIIDPHIGLLHR  318 (385)
Q Consensus       250 ~~Geg~g~vEapRG~l~h~~~~dg~g~~~r~~ir~Ps~~n~~al~~~l~G~~i~D~---V~~~dp~ig~~hR  318 (385)
                      |+|+|+|+||||||+|+|||++|++|+|++++|++||+||+++|+++++|+.++|+   +.++|||+||+.|
T Consensus       304 ~~G~g~g~vEApRG~L~H~~~~d~~g~i~~~~ii~PT~~N~~~~e~al~G~~i~D~~~iirSfDpC~sC~dr  375 (375)
T d2fug41         304 PKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR  375 (375)
T ss_dssp             CSCCCCCCBCCSSSCBCEEEECCSSSSCSEEEECCSHHHHTTTHHHHTTTSCGGGTTHHHHTTCCCHHHHHC
T ss_pred             CCcEEEEEEEcCCeEEEEEEEECCCCcEEEEEEECCCHHHHHHHHHHhCCCchHHHHHHHhcCCCcccCCCC
Confidence            89999999999999999999999999999999999999999999999999999996   4469999999876

PyMOL of d2fug41

>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]}	Back information, alignment and structure

>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]}	Back information, alignment and structure

>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]}	Back information, alignment and structure

>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]}	Back information, alignment and structure

>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]}	Back information, alignment and structure

>d2fug41 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]}	Back information, alignment and structure

>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]}	Back information, alignment and structure

>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]}	Back information, alignment and structure

>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]}	Back information, alignment and structure

>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]}	Back information, alignment and structure